--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/addssu.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,94 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified Jan 29, 2020
+
+Description:  Adds, removes, or replaces SSU sequence of existing sketches.
+Sketches and SSU fasta files must be annotated with TaxIDs.
+
+Usage:           addssu.sh in=a.sketch out=b.sketch 16S=16S.fa 18S=18S.fa
+
+Standard parameters:
+in=<file>       Input sketch file.
+out=<file>      Output sketch file.
+
+Additional files (optional):
+16S=<file>      A fasta file of 16S sequences.  These should be renamed
+                so that they start with tid|# where # is the taxID.
+                Should not contain organelle rRNA.
+18S=<file>      A fasta file of 18S sequences.  These should be renamed
+                so that they start with tid|# where # is the taxID.
+                Should not contain organelle rRNA.
+tree=auto       Path to TaxTree, if performing prok/euk-specific operations.
+
+Processing parameters:
+preferSSUMap=f
+preferSSUMapEuks=f
+preferSSUMapProks=f
+SSUMapOnly=f
+SSUMapOnlyEuks=f
+SSUMapOnlyProks=f
+clear16S=f
+clear18S=f
+clear16SEuks=f
+clear18SEuks=f
+clear16SProks=f
+clear18SProks=f
+
+
+Java Parameters:
+-Xmx            This will set Java's memory usage, overriding autodetection.
+                -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
+                    The max is typically 85% of physical memory.
+-da             Disable assertions.
+
+For more detailed information, please read /bbmap/docs/guides/BBSketchGuide.txt.
+Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
+"
+}
+
+#This block allows symlinked shellscripts to correctly set classpath.
+pushd . > /dev/null
+DIR="${BASH_SOURCE[0]}"
+while [ -h "$DIR" ]; do
+  cd "$(dirname "$DIR")"
+  DIR="$(readlink "$(basename "$DIR")")"
+done
+cd "$(dirname "$DIR")"
+DIR="$(pwd)/"
+popd > /dev/null
+
+#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
+CP="$DIR""current/"
+
+z="-Xmx4g"
+z2="-Xms4g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+		return
+	fi
+	#freeRam 3200m 84
+	#z="-Xmx${RAM}m"
+	#z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+sendsketch() {
+	local CMD="java $EA $EOOM $z -cp $CP sketch.AddSSU $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+sendsketch "$@"